Contacts of the strand formed by residues 105 - 109 (chain S) in PDB entry 2FRV
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ALA 105 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68S PHE 4.1 0.2 + - - -
69S VAL* 3.4 13.9 - - + +
70S CYS 2.8 29.6 + - - -
103S ALA* 3.3 4.3 - - - +
104S LYS* 1.3 78.5 - - + +
106S VAL* 1.3 61.7 + - - +
143S ILE* 5.1 3.8 - - + -
162S LEU* 4.1 33.0 - - + -
167S MET* 6.0 2.2 - - - -
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Residues in contact with VAL 106 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70S CYS* 3.2 11.9 - - + +
72S ILE* 3.9 29.2 - - + -
100S ALA* 3.6 27.6 - - - +
103S ALA* 4.2 4.9 - - + +
105S ALA* 1.3 79.8 - - - +
107S ILE* 1.3 68.7 + - - +
131S VAL* 4.4 1.8 - - + -
140S VAL* 3.7 26.2 - - + -
141S LYS 4.6 3.2 + - - +
142S ALA* 3.4 20.5 - - + +
143S ILE* 3.0 26.1 + - - +
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Residues in contact with ILE 107 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69S VAL* 4.4 10.5 - - + -
70S CYS 2.7 12.6 + - - +
71S VAL* 3.4 7.2 - - + +
72S ILE* 3.0 25.8 + - - +
106S VAL* 1.3 81.4 - - - +
108S ALA* 1.3 63.5 - - - +
109S ILE 3.8 1.4 + - - +
143S ILE* 3.7 14.4 - - + +
145S ILE* 3.9 22.9 - - + -
155S PHE* 3.8 23.3 - - + -
158S THR* 4.0 12.1 - - + -
159S VAL* 3.7 30.5 - - + -
162S LEU* 3.7 27.8 - - + -
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Residues in contact with ALA 108 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72S ILE* 3.7 7.2 - - - +
106S VAL 4.2 1.0 - - - -
107S ILE* 1.3 71.0 - - - +
109S ILE* 1.3 57.6 + - - +
113S ALA* 3.9 18.6 - - + +
114S THR* 3.2 10.9 - - + +
131S VAL* 4.2 8.1 - - + -
142S ALA* 3.9 12.5 - - + +
143S ILE 2.8 10.4 + - - +
144S ASN* 3.4 25.1 - - - +
145S ILE* 2.9 30.7 + - - +
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Residues in contact with ILE 109 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11S TYR* 3.5 19.3 - - - +
20S CYS* 3.7 34.2 - - + +
23S SER* 4.6 4.0 - - - +
24S VAL* 4.0 17.9 - - + -
71S VAL* 4.0 11.4 - - + -
72S ILE 3.1 11.1 + - - +
73S GLU* 3.7 22.9 - - + -
74S GLY 4.2 1.2 + - - -
107S ILE 3.8 1.0 + - - -
108S ALA* 1.3 69.1 - - - +
110S GLY* 1.3 67.7 + - - +
113S ALA* 3.5 10.6 + - - +
145S ILE* 4.0 3.8 - - + -
150S PRO* 4.0 14.4 - - + -
155S PHE* 4.0 34.1 - - + -
267S SF4 5.2 0.3 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il